Richard Lab:protocols: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
 
(120 intermediate revisions by 6 users not shown)
Line 1: Line 1:
Back to [[Richard_Lab | Richard Lab]]
Back to [[Richard_Lab | Richard Lab Main Page]]
<center>
<center>
=Equipment=
=Equipment=
</center>
</center>
==Dionex IC==
==Dionex IC==
*[[Richard Lab:IC standards]]
::'''[[Richard Lab:IC overview|Overview]]'''
::'''[[Richard Lab:IC eluents|Eluent Preparation]]'''
::'''[[Richard Lab:IC standards|Standard Preparation]]'''
==Dionex ASE==
==Dionex ASE==
*Put protocol here
::'''[[Richard Lab:ASE overview|Overview]]'''
==Anaerobic Chamber==
==Anaerobic Chamber==
*Put protocol here
::'''[[Richard Lab:anaerobic chamber|Overview]]'''
==Data Logger==
 
====To Reconfigure data into a compatible format====
==YSI Analyzer==
*The following is a set of [http://www.abe.psu.edu/bioconversion/temperature/instructions.htm instructions on how to use macros] to transform a data set from [http://www.abe.psu.edu/bioconversion/temperature/config1.htm configuration 1] to [http://www.abe.psu.edu/bioconversion/temperature/config2.htm configuration 2].
::'''[[YSI 2700 Select Biochemistry Analyzer|Overview]]
::'''[[Quantification of glucose]]


<center>
<center>
=Methods=
=Methods=
</center>
</center>
==Molecular Biology==
==Biomass Protocols==
 
=====[[Miniprep/GET_buffer | Plasmid Extraction]]=====
 
=====[[DNA_Precipitation | DNA Concentration]]=====
 
====PCR Construction====
 
====Bio-Brick Digest====
 
====Partial Digest====
 
====[[Richard_Lab:_Agarose_Gel_Electrophoresis| Agarose Gel Electrophoresis]]====
 
====Polyacrylamide Gel Electrophoresis====
 
====Gel Extraction of DNA Fragments====
 
====Ligation====
 
====Electro-transformation of ''E. coli''====
 
====Electro-transformation of Lactobacillus====
 
====Making Electro-competent Cells====
 
====Promoter Probing====
 
 
 
==Fiber Analysis==


====[http://openwetware.org/wiki/Richard_lab:NDF]====
::'''[[Silage protocols|Silage Protocols]]'''
::'''[[Biomass compositional analysis|Biomass Compositional Analysis]]'''
::'''[[Richard_Lab:_NDF|NDF (Neutral Detergent Fiber) Determination]]'''
::'''[[Richard_Lab:ADF|ADF (Acid Detergent Fiber) Determination]]'''
::'''[[Richard_Lab:ADL|ADL (Acid Detergent Lignin) Determination]]'''
::'''[[Richard Lab:Dilute-acid pretreatment|Dilute-Acid Pretreatment of Biomass]]'''
::'''[[Richard Lab:Enzymatic Hydrolysis of Biomass|Enzymatic Hydrolysis of Biomass]]'''
::'''[[Quantification of glucose|Quantification of Glucose]]'''
::'''[[Richard Lab:SSCF|Simultaneous Saccharification and Co-Fermentation (SSCF)]]'''
::'''[[SSF Ethanol production]]'''
::'''[[Acidification of C and N Samples using Tartic Acid]]'''


====[[NDF]]====
==Enzymatic Screens and Assays==


====[[ADF]]====
::'''[[Feruloyl Esterase Protocols|Ferulic Acid Esterase Protocols]]'''
::'''[[Laccase Protocols]]'''
::'''[[Xylanase Protocols]]'''
::'''[[Beta-galactosidase assay|Beta-galactosidase (LacZ) Assay]]'''
::'''[[Beta-galactosidase Screen]]
::'''[[Beta-glucuronidase protocols|Beta-glucuronidase (GusA) Protocols]]'''
::'''[[Cellulase assays]]'''


====[[ADL]]====
==Molecular/Synthetic Biology==


====TMAH Lignin Analysis====
::'''[[Richard Lab:Amplified Insert Assembly|Amplified Insert Assembly]]'''
*Put protocol here
::'''[[Richard Lab:Bio-Brick Formats|Bio-Brick Formats]]'''
====BOD, moisture and VS content====
::'''[[Richard Lab:PCR|PCR Protocols]]'''
Organic matter samples are analyzed according to the following instructions for [http://www.abe.psu.edu/bioconversion/biofilter_characterization/BOD.htm BOD (Biological Oxygen Demand)] and [http://www.abe.psu.edu/bioconversion/biofilter_characterization/moisture_and_VS.htm moisture and Volatile Solids (organic matter) content] analysis.
::'''[[Richard Lab:Site Directed Mutagenesis| Site Directed Mutagenesis]]'''
::'''[[Miniprep/GET_buffer | Plasmid Extraction]]'''
::'''[[DNA Quantification]]'''
::'''[[Ethanol_precipitation_of_nucleic_acids | DNA Concentration]]'''
::'''[[DNA Synthesis from Oligos|DNA Synthesis]]'''
::'''[[Richard_Lab:Restriction_Digest | Restriction Digestion]]'''
::'''[[Partial Restriction Digest]]'''
::'''[[Richard_Lab:_Agarose_Gel_Electrophoresis| Agarose Gel Electrophoresis]]'''
::'''[[Polyacrylamide Gel Electrophoresis]]'''
::'''[[DNA_Gel_extraction | Gel Extraction of DNA]]'''
::'''[[Richard_Lab:Ligation|Ligation]]'''
::'''[[In vitro modification of DNA for L. plantarum|Preparation of Shuttle-vectors for transformation]]'''
::'''[[Transforming Lactococcus lactis]]'''
::'''[[Richard_Lab:Preparing_electrocompetent_cells|Making Electro-competent ''E. coli'']]'''
::'''[[Richard Lab:Electroporation of E. coli|Electro-transformation of ''E. coli'']]'''
::'''[[Lactobacillus transformation (Speer 2012)|Electro-transformation of ''L. Plantarum'']]'''
::'''[[Chromosomal Integration]]'''


==Gas Analysis==
==Manure Storage and Emissions Analysis==
====Method used to measure and analyze gas fluxes from a given surface====
*gaseous emission data is collected using a [http://www.abe.psu.edu/bioconversion/gas_sampling.ppt static flux chamber and a photoacoustic sensor].
*an [http://www.abe.psu.edu/bioconversion/programPAS.xls Excel program] is then used to extract relevant data (from the continuous data collected by the photoacoustic sensor every minute). The same program also calculates the flux of selected gases from the tested surface, using Pedersen's equation (2001).
*selected data are copied and pasted as values into a compiled data set
*a regression analysis is performed to evaluate the effect of time, biofilter treatment, and other input variables on the flux level of each analyzed gas: ammonia, methane, carbon dioxide, nitrous oxide and water vapor. The Sagata Regression Pro software (ltd) is used: go to regression > pick inputs > pick outputs > chose data types (categorical or continuous) > chose regression model (to evaluate interactions create input variables made of factors evaluate for interaction amongst them, multiplied by each other) > go to output, get response vs. factors for preliminary graphs > choose indicative title for the output sheet > click ok.
*the statistical analysis output is interpreted: the first Anova table shows possible treatment effect. The "term significance" table shows effect of individual factors (or interactions). 


====Method used to set up biofilters on a surface in the field====
::'''[[Richard Lab:Gas_Flux|Measuring and Analyzing Gas-Flux from a Surface]]'''
[http://www.abe.psu.edu/bioconversion/biofilters_setup.ppt How biofilters are set up].
::'''[http://www.abe.psu.edu/bioconversion/biofilters_setup.ppt Setting Up Biofilters in the Field].
::'''Formatting Data from Data Logger'''
:::*The following is a set of [http://www.abe.psu.edu/bioconversion/temperature/instructions.htm instructions on how to use macros] to transform a data set from [http://www.abe.psu.edu/bioconversion/temperature/config1.htm configuration 1] to [http://www.abe.psu.edu/bioconversion/temperature/config2.htm configuration 2].
::'''BOD, moisture and VS content'''
:::*Organic matter samples are analyzed according to the following instructions for [http://www.abe.psu.edu/bioconversion/biofilter_characterization/BOD.htm BOD (Biological Oxygen Demand)] and [http://www.abe.psu.edu/bioconversion/biofilter_characterization/moisture_and_VS.htm moisture and Volatile Solids (organic matter) content] analysis.


==Compost Analysis==
::'''[[Chemical Oxygen Demand]]'''
::'''[[Compost Pile Monitoring]]'''
::'''[[CO2 Respiration]]'''
::'''[[Manure and Compost Sampling Preparation Protocols]]'''
::'''[[Acidification of compost with 0.5 N HCl]]'''
::'''[[Free Air Space Testing Procedure]]'''
Back to [[Richard_Lab | Richard Lab]]
Back to [[Richard_Lab | Richard Lab]]

Latest revision as of 13:35, 10 January 2012

Back to Richard Lab Main Page

Equipment

Dionex IC

Overview
Eluent Preparation
Standard Preparation

Dionex ASE

Overview

Anaerobic Chamber

Overview

YSI Analyzer

Overview
Quantification of glucose

Methods

Biomass Protocols

Silage Protocols
Biomass Compositional Analysis
NDF (Neutral Detergent Fiber) Determination
ADF (Acid Detergent Fiber) Determination
ADL (Acid Detergent Lignin) Determination
Dilute-Acid Pretreatment of Biomass
Enzymatic Hydrolysis of Biomass
Quantification of Glucose
Simultaneous Saccharification and Co-Fermentation (SSCF)
SSF Ethanol production
Acidification of C and N Samples using Tartic Acid

Enzymatic Screens and Assays

Ferulic Acid Esterase Protocols
Laccase Protocols
Xylanase Protocols
Beta-galactosidase (LacZ) Assay
Beta-galactosidase Screen
Beta-glucuronidase (GusA) Protocols
Cellulase assays

Molecular/Synthetic Biology

Amplified Insert Assembly
Bio-Brick Formats
PCR Protocols
Site Directed Mutagenesis
Plasmid Extraction
DNA Quantification
DNA Concentration
DNA Synthesis
Restriction Digestion
Partial Restriction Digest
Agarose Gel Electrophoresis
Polyacrylamide Gel Electrophoresis
Gel Extraction of DNA
Ligation
Preparation of Shuttle-vectors for transformation
Transforming Lactococcus lactis
Making Electro-competent E. coli
Electro-transformation of E. coli
Electro-transformation of L. Plantarum
Chromosomal Integration

Manure Storage and Emissions Analysis

Measuring and Analyzing Gas-Flux from a Surface
Setting Up Biofilters in the Field.
Formatting Data from Data Logger
BOD, moisture and VS content

Compost Analysis

Chemical Oxygen Demand
Compost Pile Monitoring
CO2 Respiration
Manure and Compost Sampling Preparation Protocols
Acidification of compost with 0.5 N HCl
Free Air Space Testing Procedure

Back to Richard Lab

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Richard_Lab:protocols&oldid=575371"